#ifdef _WIN32
#pragma warning(disable:4164 4003)
#endif 
# 1 "smithwaterman.cudafe1.gpu"
# 14 "../typedefs.h"
struct LocalMatrix;
# 19 "../typedefs.h"
struct ScoringsMatrix;
# 24 "../typedefs.h"
struct GlobalMatrix;
# 28 "../typedefs.h"
struct BlockMaxima;
# 32 "../typedefs.h"
struct GlobalMaxima;
# 36 "../typedefs.h"
struct LocalDirection;
# 40 "../typedefs.h"
struct Direction;
# 44 "../typedefs.h"
struct GlobalDirection;
# 48 "../typedefs.h"
struct StartingPoint;
# 60 "../typedefs.h"
struct StartingPoints;
# 211 "/usr/lib/gcc/x86_64-linux-gnu/4.4.5/include/stddef.h" 3
typedef unsigned long size_t;
#include "crt/host_runtime.h"
# 145 "/usr/include/bits/types.h" 3
typedef long __clock_t;
# 60 "/usr/include/time.h" 3
typedef __clock_t clock_t;
# 14 "../typedefs.h"
struct LocalMatrix {
# 15 "../typedefs.h"
float value[8][8];};
# 16 "../typedefs.h"
typedef struct LocalMatrix LocalMatrix;
# 19 "../typedefs.h"
struct ScoringsMatrix {
# 20 "../typedefs.h"
LocalMatrix matrix[58][15];};
# 21 "../typedefs.h"
typedef struct ScoringsMatrix ScoringsMatrix;
# 24 "../typedefs.h"
struct GlobalMatrix {
# 25 "../typedefs.h"
ScoringsMatrix metaMatrix[25][323];};
# 26 "../typedefs.h"
typedef struct GlobalMatrix GlobalMatrix;
# 28 "../typedefs.h"
struct BlockMaxima {
# 29 "../typedefs.h"
float value[58][15];};
# 30 "../typedefs.h"
typedef struct BlockMaxima BlockMaxima;
# 32 "../typedefs.h"
struct GlobalMaxima {
# 33 "../typedefs.h"
BlockMaxima blockMaxima[25][323];};
# 34 "../typedefs.h"
typedef struct GlobalMaxima GlobalMaxima;
# 36 "../typedefs.h"
struct LocalDirection {
# 37 "../typedefs.h"
unsigned char value[8][8];};
# 38 "../typedefs.h"
typedef struct LocalDirection LocalDirection;
# 40 "../typedefs.h"
struct Direction {
# 41 "../typedefs.h"
LocalDirection localDirection[58][15];};
# 42 "../typedefs.h"
typedef struct Direction Direction;
# 44 "../typedefs.h"
struct GlobalDirection {
# 45 "../typedefs.h"
Direction direction[25][323];};
# 46 "../typedefs.h"
typedef struct GlobalDirection GlobalDirection;
# 48 "../typedefs.h"
struct StartingPoint {
# 49 "../typedefs.h"
unsigned sequence;
# 50 "../typedefs.h"
unsigned target;
# 51 "../typedefs.h"
unsigned blockX;
# 52 "../typedefs.h"
unsigned blockY;
# 53 "../typedefs.h"
unsigned valueX;
# 54 "../typedefs.h"
unsigned valueY;
# 55 "../typedefs.h"
float score;
# 56 "../typedefs.h"
float maxScore;
# 57 "../typedefs.h"
float posScore;};
# 58 "../typedefs.h"
typedef struct StartingPoint StartingPoint;
# 60 "../typedefs.h"
struct StartingPoints {
# 61 "../typedefs.h"
StartingPoint startingPoint[8075000];};
# 62 "../typedefs.h"
typedef struct StartingPoints StartingPoints;
void *memcpy(void*, const void*, size_t); void *memset(void*, int, size_t);
#include "smithwaterman.cudafe2.stub.h"
# 88 "../definitions.h"
__loc_sc__(__constant__,,) float __shadow_var(scoringsMatrix,scoringsMatrix)[26][26];

#include "smithwaterman.cudafe2.stub.c"
